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Do you know how to get the alpha of clouds to render? Ive tried for a whole day and cant seem to do it. The alpha just winds up totally black. I need to render the clouds seperatly from the atmostphere background.

It's a multipass feature. At the very bottom of the multipass dialog you'll see it. Checking this will save both the color and alpha of cloud layers. As of 9.5 you still can't save individual cloud layers unfortunately.

Seeing the glass as half empty is being an optimist when the glass is full of urine